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Yorodumi- EMDB-13931: High-resolution structure of the Anaphase-promoting complex/cyclo... -
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-Basic information
Entry | Database: EMDB / ID: EMD-13931 | |||||||||
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Title | High-resolution structure of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-activator Cdh1 | |||||||||
Map data | Overall map (sharpened with deepEMhancer) of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 at 2.9 A resolution. | |||||||||
Sample |
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Keywords | APC/C / cyclosome / Cdc20 / Cdh1 / ubiquitination / Emi1 / mitosis / Cell cycle | |||||||||
Function / homology | Function and homology information negative regulation of DNA endoreduplication / positive regulation of biomineral tissue development / negative regulation of meiotic nuclear division / positive regulation of anaphase-promoting complex-dependent catabolic process / negative regulation of mitotic metaphase/anaphase transition / positive regulation of mesenchymal stem cell migration / regulation of meiotic nuclear division / Mitotic Metaphase/Anaphase Transition / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase ...negative regulation of DNA endoreduplication / positive regulation of biomineral tissue development / negative regulation of meiotic nuclear division / positive regulation of anaphase-promoting complex-dependent catabolic process / negative regulation of mitotic metaphase/anaphase transition / positive regulation of mesenchymal stem cell migration / regulation of meiotic nuclear division / Mitotic Metaphase/Anaphase Transition / positive regulation of synapse maturation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / regulation of mitotic cell cycle spindle assembly checkpoint / vesicle organization / protein branched polyubiquitination / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Phosphorylation of Emi1 / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / metaphase/anaphase transition of mitotic cell cycle / lens fiber cell differentiation / positive regulation of synaptic plasticity / regulation of exit from mitosis / anaphase-promoting complex binding / Phosphorylation of the APC/C / negative regulation of ubiquitin-protein transferase activity / positive regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin protein ligase activity / ubiquitin ligase activator activity / spindle assembly involved in female meiosis I / protein K11-linked ubiquitination / meiotic spindle / enzyme-substrate adaptor activity / positive regulation of dendrite morphogenesis / regulation of mitotic metaphase/anaphase transition / oocyte maturation / ubiquitin-ubiquitin ligase activity / negative regulation of ubiquitin protein ligase activity / regulation of mitotic nuclear division / mitotic metaphase chromosome alignment / molecular function inhibitor activity / G1/S-Specific Transcription / regulation of DNA replication / mitotic G2 DNA damage checkpoint signaling / negative regulation of cellular senescence / microtubule polymerization / Regulation of APC/C activators between G1/S and early anaphase / cullin family protein binding / ubiquitin ligase inhibitor activity / Transcriptional Regulation by VENTX / ubiquitin-like ligase-substrate adaptor activity / positive regulation of axon extension / protein K48-linked ubiquitination / positive regulation of osteoblast differentiation / heterochromatin / Cyclin A:Cdk2-associated events at S phase entry / regulation of mitotic cell cycle / positive regulation of G2/M transition of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / nuclear periphery / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / brain development / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / mitotic spindle / CDK-mediated phosphorylation and removal of Cdc6 / kinetochore / spindle / ubiquitin-protein transferase activity / Separation of Sister Chromatids / microtubule cytoskeleton / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / mitotic cell cycle / nervous system development / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein phosphatase binding / nuclear membrane / molecular adaptor activity / cell differentiation / protein ubiquitination / cell division / negative regulation of gene expression / DNA repair / centrosome / DNA damage response / ubiquitin protein ligase binding / positive regulation of cell population proliferation / nucleolus / protein kinase binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Hoefler A / Yu J | |||||||||
Funding support | Switzerland, United Kingdom, 2 items
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Citation | Journal: To Be Published Title: High-resolution structure of the Anaphase-promoting complex (APC/C) bound to co-activator Cdh1 Authors: Hoefler A / Yu J / Chang L / Zhang Z / Yang J / Boland A / Barford D | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13931.map.gz | 158.7 MB | EMDB map data format | |
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Header (meta data) | emd-13931-v30.xml emd-13931.xml | 45 KB 45 KB | Display Display | EMDB header |
Images | emd_13931.png | 64.2 KB | ||
Filedesc metadata | emd-13931.cif.gz | 13 KB | ||
Others | emd_13931_additional_1.map.gz emd_13931_half_map_1.map.gz emd_13931_half_map_2.map.gz | 89.1 MB 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13931 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13931 | HTTPS FTP |
-Related structure data
Related structure data | 7qe7 9gawMC 8pkpC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13931.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Overall map (sharpened with deepEMhancer) of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 at 2.9 A resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Overall map (unsharpened) of the Anaphase-promoting complex/cyclosome (APC/C)...
File | emd_13931_additional_1.map | ||||||||||||
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Annotation | Overall map (unsharpened) of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 at 2.9 A resolution. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B of the Anaphase-promoting complex/cyclosome (APC/C)...
File | emd_13931_half_map_1.map | ||||||||||||
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Annotation | Half map B of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 at 2.9 A resolution. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A of the Anaphase-promoting complex/cyclosome (APC/C)...
File | emd_13931_half_map_2.map | ||||||||||||
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Annotation | Half map A of the Anaphase-promoting complex/cyclosome (APC/C) bound to co-factor Cdh1 at 2.9 A resolution. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
+Supramolecule #1: Anaphase-promoting complex (APC/C) bound to co-activator Cdh1
+Macromolecule #1: Anaphase-promoting complex subunit 10
+Macromolecule #2: Anaphase-promoting complex subunit 15
+Macromolecule #3: Anaphase-promoting complex subunit 1
+Macromolecule #4: Anaphase-promoting complex subunit 2
+Macromolecule #5: Anaphase-promoting complex subunit 4
+Macromolecule #6: Anaphase-promoting complex subunit 5
+Macromolecule #7: F-box only protein 5
+Macromolecule #8: Cell division cycle protein 16 homolog
+Macromolecule #9: Anaphase-promoting complex subunit CDC26
+Macromolecule #10: Anaphase-promoting complex subunit 13
+Macromolecule #11: Anaphase-promoting complex subunit 16
+Macromolecule #12: Cell division cycle protein 27 homolog
+Macromolecule #13: Anaphase-promoting complex subunit 7
+Macromolecule #14: Cell division cycle protein 23 homolog
+Macromolecule #15: Fizzy-related protein homolog
+Macromolecule #16: Anaphase-promoting complex subunit 11
+Macromolecule #17: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 50 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: OTHER | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 8297 / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm |
Sample stage | Specimen holder model: OTHER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 80 |
Output model |
PDB-7qe7: PDB-9gaw: |